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New Tools for Monitoring Genetic Diversity in Animals

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A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 13682

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Special Issue Editors

Dr. Giovanni Forcina

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Guest Editor

CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, 4485-661 Vairão, Portugal
Interests: animal production; conservation genomics; wildlife forensics; evolutionary biology; ancient DNA

Dr. Qian Tang

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Guest Editor

Department of Biological Sciences, The National University of Singapore, Singapore 117558, Singapore
Interests: population genetics; evolutionary biology; landscape genetics; ecology; conservation; biological invasions

Dr. María Pilar Cabezas Rodríguez

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Biogeographical Ecology and Evolution, CCMAR - Centro de Ciências do Mar, University of Algarve, 8005-139 Faro, Portugal
Interests: changes in species distribution and their relation with human activity; cryptic species; DNA metabarcoding; marine biodiversity; monitoring; morphological and molecular taxonomy of marine invertebrates; next-generation sequencing; non-indigenous species

Special Issue Information

Dear Colleagues,

Recent years have witnessed unprecedented changes in all life sciences as a result of major advances in molecular biology coupled with the sharp decrease of costs to generate massive amounts of genomic data. Fostered by the fast-growing availability of freely accessible genome resources as reference, the feasibility of applying high-throughput approaches to multiple individuals triggered a virtuous circle which generates more and more data for the scientific community to produce new and increasingly comprehensive studies.

In this Special Issue, we invite contributions that show how these epochal changes have revolutionized the research on animals, spanning disciplines as wide ranging as conservation, evolution, and ecology. The scope of this Issue is to keep track of the plethora of new tools being used in animal research over time while focusing on possible differences between the results previously obtained with traditional marker systems.

Of particular interest is the discussion about how former results were questioned by the new ones and on the underlying implications as well as on recommendations for mutual research efforts to fill the existing knowledge gaps. Topics may include (but are not limited to) animal evolution, ecology, physiology, conservation, wildlife population biology, wildlife forensics, and zootechny.

Dr. Giovanni Forcina
Dr. Qian Tang
Dr. María Pilar Cabezas Rodríguez
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

genomic revolution
high-throughput technologies
reduced representation methods
phylogenomics
whole-genome sequencing
next-generation sequencing
genomic library
genetic diversity
biodiversity monitoring
introgression

Published Papers (9 papers)

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Research

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15 pages, 4197 KiB

Open AccessArticle

Small-Mammal Genomics Highlights Viaducts as Potential Dispersal Conduits for Fragmented Populations

by Tabitha C. Y. Hui, Qian Tang, Elize Y. X. Ng, Ju Lian Chong, Eleanor M. Slade and Frank E. Rheindt

Animals 2024, 14(3), 426; https://0-doi-org.brum.beds.ac.uk/10.3390/ani14030426 - 28 Jan 2024

Viewed by 622

Abstract

Wildlife crossings are implemented in many countries to facilitate the dispersal of animals among habitats fragmented by roads. However, the efficacy of different types of habitat corridors remains poorly understood. We used a comprehensive sampling regime in two lowland dipterocarp forest areas in peninsular Malaysia to sample pairs of small mammal individuals in three treatment types: (1) viaduct sites, at which sampling locations were separated by a highway but connected by a vegetated viaduct; (2) non-viaduct sites, at which sampling locations were separated by a highway and not connected by a viaduct; and (3) control sites, at which there was no highway fragmenting the forest. For four small mammal species, the common tree shrew Tupaia glis, Rajah’s spiny rat Maxomys rajah, Whitehead’s spiny rat Maxomys whiteheadi and dark-tailed tree rat Niviventer cremoriventer, we used genome-wide markers to assess genetic diversity, gene flow and genetic structure. The differences in genetic distance across sampling settings among the four species indicate that they respond differently to the presence of highways and viaducts. Viaducts connecting forests separated by highways appear to maintain higher population connectivity than forest fragments without viaducts, at least in M. whiteheadi, but apparently not in the other species. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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24 pages, 3318 KiB

Open AccessArticle

Assessing the Seasonal and Spatial Dynamics of Zooplankton through DNA Metabarcoding in a Temperate Estuary

by Jorge Moutinho, Diego Carreira-Flores, Pedro T. Gomes, Filipe O. Costa and Sofia Duarte

Animals 2023, 13(24), 3876; https://0-doi-org.brum.beds.ac.uk/10.3390/ani13243876 - 16 Dec 2023

Viewed by 1257

Abstract

Zooplankton are key components of estuarine trophic networks. However, routine monitoring is hindered by the difficulty of morphology-based identification. DNA-based methods allow us to circumvent some of these hurdles, providing precise species identifications regardless of the taxonomic expertise of the investigator or the developmental stage of the specimens. However, the process is dependent on the completeness of the reference libraries. In this study, we sought to evaluate the potential of DNA metabarcoding to assess the seasonal (summer, autumn, and early spring) and spatial dynamics of zooplankton (four locations spanning ca. 6 km) in the Lima estuary (NW Portugal). Two genetic markers were used: the cytochrome c oxidase subunit I and the V4 hypervariable region of the ribosomal 18S rRNA genes. Overall, 327 species were recovered, and both markers displayed minute overlap (7% were detected with both markers). Species richness, composition, and taxonomic distinctness were majorly influenced by the season, with a declining tendency from summer (highest number of exclusive species, n = 74) to spring. Second to season, the taxa composition was influenced by spatial variation where the most downstream site displayed the highest number of exclusive species, n = 53. A total of 16 non-indigenous species were detected using metabarcoding, but only one (Austrominus modestus) has been documented out in the estuary. In conclusion, both the seasonal and spatial gradients influenced the recovered richness, composition, and taxonomic distinctness, confirming the great aptitude of DNA metabarcoding for providing higher density monitoring and shedding new light on the composition and dynamics of complex zooplankton communities. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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15 pages, 1520 KiB

Open AccessArticle

Comprehensive Gene Expression Profiling Analysis of Adipose Tissue in Male Individuals from Fat- and Thin-Tailed Sheep Breeds

by Sana Farhadi, Karim Hasanpur, Jalil Shodja Ghias, Valiollah Palangi, Aristide Maggiolino and Vincenzo Landi

Animals 2023, 13(22), 3475; https://0-doi-org.brum.beds.ac.uk/10.3390/ani13223475 - 10 Nov 2023

Viewed by 931

Abstract

It has been shown that tail fat content varies significantly among sheep breeds and plays a significant role in meat quality. Recently, significant efforts have been made to understand the physiological, biochemical, and genomic regulation of fat deposition in sheep tails in order to unravel the mechanisms underlying energy storage and adipose tissue lipid metabolism. RNA-seq has enabled us to provide a high-resolution snapshot of differential gene expression between fat- and thin-tailed sheep breeds. Therefore, three RNA-seq datasets were meta-analyzed for the current work to elucidate the transcriptome profile differences between them. Specifically, we identified hub genes, performed gene ontology (GO) analysis, carried out enrichment analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and validated hub genes using machine learning algorithms. This approach revealed a total of 136 meta-genes, 39 of which were not significant in any of the individual studies, indicating the higher statistical power of the meta-analysis. Furthermore, the results derived from the use of machine learning revealed POSTN, K35, SETD4, USP29, ANKRD37, RTN2, PRG4, and LRRC4C as substantial genes that were assigned a higher weight (0.7) than other meta-genes. Among the decision tree models, the Random Forest ones surpassed the others in adipose tissue predictive power fat deposition in fat- and thin-tailed breeds (accuracy > 0.85%). In this regard, combining meta-analyses and machine learning approaches allowed for the identification of three important genes (POSTN, K35, SETD4) related to lipid metabolism, and our findings could help animal breeding strategies optimize fat-tailed breeds’ tail sizes. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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22 pages, 6388 KiB

Open AccessArticle

Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds

by Natalia A. Volkova, Michael N. Romanov, Alexandra S. Abdelmanova, Polina V. Larionova, Nadezhda Yu. German, Anastasia N. Vetokh, Alexey V. Shakhin, Ludmila A. Volkova, Dmitry V. Anshakov, Vladimir I. Fisinin, Valeriy G. Narushin, Darren K. Griffin, Johann Sölkner, Gottfried Brem, John C. McEwan, Rudiger Brauning and Natalia A. Zinovieva

Animals 2023, 13(22), 3439; https://0-doi-org.brum.beds.ac.uk/10.3390/ani13223439 - 07 Nov 2023

Cited by 2 | Viewed by 846

Abstract

Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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14 pages, 3346 KiB

Open AccessArticle

Wild Avian Gut Microbiome at a Small Spatial Scale: A Study from a Mediterranean Island Population of Alectoris rufa

by Monica Guerrini, Dalia Tanini, Claudia Vannini and Filippo Barbanera

Animals 2023, 13(21), 3341; https://0-doi-org.brum.beds.ac.uk/10.3390/ani13213341 - 27 Oct 2023

Viewed by 995

Abstract

This research is one of the few comparative descriptions at an intraspecific level of wild non-passerine microbiomes. We investigated for the first time the gut microbiome of red-legged partridges (Alectoris rufa) using fecal pellets in order to provide a more informed management. We focused on a small Italian population consisting of two demes (WEST, EAST) separated by about 20 km on the opposite sides of Elba Island. Given the small spatial scale, we set up a sampling protocol to minimize contamination from environmental bacteria, as well as differences due to variations in—among others—habitat, season, and age of feces, that could possibly affect the investigation of the three Elban sites. We found a significant divergence between the WEST and EAST Elban subpopulations in terms of microbial composition and alpha diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher diversity in western than in eastern partridges. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. We suggest that the two subpopulations should be treated as distinct management units. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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13 pages, 1999 KiB

Open AccessArticle

Developing Methods for Maintaining Genetic Diversity in Novel Aquaculture Species: The Case of Seriola lalandi

by Víctor Martinez, Nicolas Galarce and Alvin Setiawan

Animals 2023, 13(5), 913; https://0-doi-org.brum.beds.ac.uk/10.3390/ani13050913 - 02 Mar 2023

Viewed by 1563

Abstract

Developing sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as well as a 90 K SNP genotyping array based on different populations of yellowtail kingfish (Seriola lalandi). The minimum and maximum distance between adjacent marker pairs were 0.7 Mb and 13 Mb, respectively, with an average marker spacing of 2 Mb. Weak evidence of the linkage disequilibrium between adjacent marker pairs was found. The results showed high panel performance for parental assignment, with probability exclusion values equaling 1. The rate of false positives when using cross-population data was null. A skewed distribution of genetic contributions by dominant females was observed, thus increasing the risk of higher rates of inbreeding in subsequent captive generations when no parentage data are used. All these results are discussed in the context of breeding program design, using this marker panel to increase the sustainability of this aquaculture resource. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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11 pages, 1297 KiB

Open AccessArticle

Assessing Molecular Diversity in Native and Introduced Populations of Red Wood Ant Formica paralugubris

by Alberto Masoni, Andrea Coppi, Paride Balzani, Filippo Frizzi, Renato Fani, Marco Zaccaroni and Giacomo Santini

Animals 2022, 12(22), 3165; https://0-doi-org.brum.beds.ac.uk/10.3390/ani12223165 - 16 Nov 2022

Cited by 2 | Viewed by 1045

Abstract

The Formica rufa group comprises several ant species which are collectively referred to as “red wood ants” and play key roles in boreal forest ecosystems, where they are ecologically dominant and greatly influence habitat dynamics. Owing to their intense predatory activity, some of these species are used as biocontrol agents against several forest insect pests and for this aim in Italy, nearly 6000 ant nests were introduced from their native areas in the Alps to several Appeninic sites during the last century. In this work, we assessed and compared the genetic variability and structure of native and introduced populations of F. paralugubris, thus evaluating the extent of genetic drift that may have occurred since the time of introduction, using amplified fragment length polymorphism (AFLP) markers. PCR amplification with a fam_EcoRI-TAC/MseI-ATG primers combination produced a total of 147 scorable bands, with 17 identified as outlier loci. The genetic variation was higher in the introduced population compared to the native ones that, on the other hand, showed a higher diversity between nests. AMOVA results clearly pointed out that the overall genetic structure was dominated by among-worker variation, considering all populations, the Alpine vs. Apennine groups and the comparison among native and related introduced populations (all ranging between 77.84% and 79.84%). Genetic analyses unveiled the existence of six main different groups that do not entirely mirror their geographic subdivision, pointing towards a wide admixture between populations, but, at the same time, rapid diversification of some Apennine populations. Future studies based on high-throughput genomic methods are needed to obtain a thorough understanding of the effects of environmental pressure on the genetic structure and mating system of these populations. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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8 pages, 592 KiB

Open AccessCommunication

“Guess Who’s Coming to Dinner”: Molecular Tools to Reconstruct multilocus Genetic Profiles from Wild Canid Consumption Remains

by Edoardo Velli, Federica Mattucci, Lorenzo Lazzeri, Elena Fabbri, Giada Pacini, Irene Belardi, Nadia Mucci and Romolo Caniglia

Animals 2022, 12(18), 2428; https://0-doi-org.brum.beds.ac.uk/10.3390/ani12182428 - 15 Sep 2022

Viewed by 1474

Abstract

Non-invasive genetic sampling is a practical tool to monitor pivotal ecological parameters and population dynamic patterns of endangered species. It can be particularly suitable when applied to elusive carnivores such as the Apennine wolf (Canis lupus italicus) and the European wildcat (Felis silvestris silvestris), which can live in overlapping ecological contexts and sometimes share their habitats with their domestic free-ranging relatives, increasing the risk of anthropogenic hybridisation. In this case study, we exploited all the ecological and genetic information contained in a single biological canid faecal sample, collected in a forested area of central Italy, to detect any sign of trophic interactions between wolves and European wildcats or their domestic counterparts. Firstly, the faecal finding was morphologically examined, showing the presence of felid hair and claw fragment remains. Subsequently, total genomic DNA contained in the hair and claw samples was extracted and genotyped, through a multiple-tube approach, at canid and felid diagnostic panels of microsatellite loci. Finally, the obtained individual multilocus genotypes were analysed with reference wild and domestic canid and felid populations to assess their correct taxonomic status using Bayesian clustering procedures. Assignment analyses classified the genotype obtained from the endothelial cells present on the hair sample as a wolf with slight signals of dog ancestry, showing a qi = 0.954 (C.I. 0.780–1.000) to the wolf cluster, and the genotype obtained from the claw as a domestic cat, showing a qi = 0.996 (95% C.I. = 0.982–1.000) to the domestic cat cluster. Our results clearly show how a non-invasive multidisciplinary approach allows the cost-effective identification of both prey and predator genetic profiles and their taxonomic status, contributing to the improvement of our knowledge about feeding habits, predatory dynamics, and anthropogenic hybridisation risk in threatened species. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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Review

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19 pages, 1237 KiB

Open AccessReview

Gut Microbiome Studies in Livestock: Achievements, Challenges, and Perspectives

by Giovanni Forcina, Lucía Pérez-Pardal, Júlio Carvalheira and Albano Beja-Pereira

Animals 2022, 12(23), 3375; https://0-doi-org.brum.beds.ac.uk/10.3390/ani12233375 - 30 Nov 2022

Cited by 5 | Viewed by 3230

Abstract

The variety and makeup of the gut microbiome are frequently regarded as the primary determinants of health and production performances in domestic animals. High-throughput DNA/RNA sequencing techniques (NGS) have recently gained popularity and permitted previously unheard-of advancements in the study of gut microbiota, particularly for determining the taxonomic composition of such complex communities. Here, we summarize the existing body of knowledge on livestock gut microbiome, discuss the state-of-the-art in sequencing techniques, and offer predictions for next research. We found that the enormous volumes of available data are biased toward a small number of globally distributed and carefully chosen varieties, while local breeds (or populations) are frequently overlooked despite their demonstrated resistance to harsh environmental circumstances. Furthermore, the bulk of this research has mostly focused on bacteria, whereas other microbial components such as protists, fungi, and viruses have received far less attention. The majority of these data were gathered utilizing traditional metabarcoding techniques that taxonomically identify the gut microbiota by analyzing small portions of their genome (less than 1000 base pairs). However, to extend the coverage of microbial genomes for a more precise and thorough characterization of microbial communities, a variety of increasingly practical and economical shotgun techniques are currently available. Full article

(This article belongs to the Special Issue New Tools for Monitoring Genetic Diversity in Animals)

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